Package Bio :: Package config :: Module SeqDBRegistry
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Module SeqDBRegistry

source code

This module handles seqdatabase.INI file.

Classes: SeqDBRegistry Holds databases from seqdatabase.INI.

Classes [hide private]
  SeqDBRegistry
This object implements a dictionary-like interface to sequence databases.
Functions [hide private]
 
_warn(message) source code
 
_load_registry_objects(ini_file) source code
 
_make_biofetch_db(name, tagvalue_dict) source code
 
_make_biosql_db(name, tagvalue_dict)
Register a BioSQL database defined in the registry.
source code
 
_make_flat_db(name, tagvalue_dict)
Register a Berkeley or Flat indexed file defined in the registry.
source code
 
_openfu(file_or_url)
Guess whether this is a file or url and open it.
source code
list of URL's or paths to search for files
_list_ini_paths()
The default places to look for registry files are:
source code
list of files to search (in order)
_list_ini_files(filename) source code
Variables [hide private]
  seqdb = seqdb
Function Details [hide private]

_list_ini_paths()

source code 

The default places to look for registry files are:

  • ${HOME}/.bioinformatics
  • /etc/bioinformatics
  • http://www.open-bio.org/registry

    The OBDA_SEARCH_PATH environment variable, if specified, overrides the default. This should be a "+" separated list of paths or URL's.

Returns: list of URL's or paths to search for files